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Magnesium in PDB 2c3o: Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus

Enzymatic activity of Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus

All present enzymatic activity of Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus:
1.2.7.1;

Protein crystallography data

The structure of Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus, PDB code: 2c3o was solved by C.Cavazza, C.Contreras-Martel, L.Pieulle, E.Chabriere, E.C.Hatchikian, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.11 / 2.7
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.650, 145.236, 204.293, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26.8

Other elements in 2c3o:

The structure of Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus also contains other interesting chemical elements:

Iron (Fe) 24 atoms
Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus (pdb code 2c3o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus, PDB code: 2c3o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2c3o

Go back to Magnesium Binding Sites List in 2c3o
Magnesium binding site 1 out of 2 in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2237

b:16.9
occ:1.00
O1B A:TPP2236 2.0 27.6 1.0
OD1 A:ASP963 2.0 19.9 1.0
O A:VAL993 2.1 23.6 1.0
O2A A:TPP2236 2.1 28.3 1.0
O A:HOH2209 2.3 24.6 1.0
OG1 A:THR991 2.5 20.7 1.0
C A:VAL993 3.0 26.1 1.0
CG A:ASP963 3.1 18.2 1.0
PB A:TPP2236 3.1 26.5 1.0
O3A A:TPP2236 3.1 27.6 1.0
PA A:TPP2236 3.2 23.9 1.0
OD2 A:ASP963 3.5 16.8 1.0
N A:VAL993 3.7 22.5 1.0
N A:SER995 3.8 26.9 1.0
N A:TYR994 3.8 28.6 1.0
CB A:THR991 3.9 20.2 1.0
OG A:SER995 3.9 14.5 1.0
O2B A:TPP2236 3.9 27.4 1.0
CA A:TYR994 4.0 28.5 1.0
N A:ASP963 4.0 16.7 1.0
CA A:VAL993 4.0 24.2 1.0
O7 A:TPP2236 4.0 29.7 1.0
N A:GLY964 4.1 14.3 1.0
O3B A:TPP2236 4.2 27.5 1.0
N A:THR991 4.3 18.1 1.0
O1A A:TPP2236 4.3 24.5 1.0
CB A:ASP963 4.3 15.1 1.0
C A:TYR994 4.4 29.2 1.0
CG2 A:THR991 4.4 20.9 1.0
CA A:THR991 4.5 21.4 1.0
C A:THR991 4.5 22.3 1.0
CB A:SER995 4.6 23.0 1.0
CA A:ASP963 4.6 17.8 1.0
N A:GLU992 4.6 21.2 1.0
CA A:GLY962 4.7 10.7 1.0
C A:GLY962 4.7 12.7 1.0
CA A:SER995 4.8 23.7 1.0
CG1 A:VAL993 4.8 17.8 1.0
O A:MET989 4.9 20.0 1.0
C A:ASP963 4.9 17.5 1.0
C A:GLU992 4.9 23.9 1.0
O A:THR991 4.9 24.6 1.0
C7 A:TPP2236 4.9 28.8 1.0

Magnesium binding site 2 out of 2 in 2c3o

Go back to Magnesium Binding Sites List in 2c3o
Magnesium binding site 2 out of 2 in the Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase From Desulfovibrio Africanus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2237

b:3.9
occ:1.00
OD1 B:ASP963 1.9 10.9 1.0
OG1 B:THR991 2.1 8.7 1.0
O B:VAL993 2.1 2.9 1.0
O B:HOH2255 2.1 2.1 1.0
O1B B:TPP2236 2.2 3.5 1.0
O2A B:TPP2236 2.4 19.2 1.0
CG B:ASP963 3.1 8.1 1.0
O3A B:TPP2236 3.1 14.5 1.0
PB B:TPP2236 3.2 14.6 1.0
C B:VAL993 3.3 8.8 1.0
PA B:TPP2236 3.3 21.1 1.0
CB B:THR991 3.5 6.6 1.0
OD2 B:ASP963 3.7 12.5 1.0
N B:ASP963 3.7 9.5 1.0
O2B B:TPP2236 3.7 7.2 1.0
N B:VAL993 4.0 15.0 1.0
N B:GLY964 4.0 12.3 1.0
N B:SER995 4.0 8.8 1.0
N B:THR991 4.1 8.2 1.0
N B:TYR994 4.1 12.5 1.0
CA B:TYR994 4.1 10.8 1.0
OG B:SER995 4.2 13.1 1.0
CG2 B:THR991 4.2 2.3 1.0
CA B:THR991 4.2 10.1 1.0
CA B:VAL993 4.2 10.3 1.0
CB B:ASP963 4.3 8.7 1.0
O7 B:TPP2236 4.3 20.3 1.0
O1A B:TPP2236 4.3 18.4 1.0
CA B:GLY962 4.3 7.8 1.0
C B:GLY962 4.4 7.7 1.0
CA B:ASP963 4.4 9.8 1.0
O3B B:TPP2236 4.5 7.5 1.0
C B:THR991 4.5 14.4 1.0
N B:GLU992 4.6 17.8 1.0
C B:TYR994 4.6 11.3 1.0
O B:MET989 4.7 21.5 1.0
C B:ASP963 4.7 11.5 1.0
CB B:SER995 4.8 12.3 1.0
CA B:GLY964 4.9 7.4 1.0
CG1 B:VAL993 4.9 4.1 1.0

Reference:

C.Cavazza, C.Contreras-Martel, L.Pieulle, E.Chabriere, E.C.Hatchikian, J.C.Fontecilla-Camps. Flexibility of Thiamine Diphosphate Revealed By Kinetic Crystallographic Studies of the Reaction of Pyruvate-Ferredoxin Oxidoreductase with Pyruvate. Structure V. 14 217 2006.
ISSN: ISSN 0969-2126
PubMed: 16472741
DOI: 10.1016/J.STR.2005.10.013
Page generated: Tue Aug 13 22:09:47 2024

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